Starting phenix.real_space_refine
on Wed Aug  5 08:35:40 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhe_49410/08_2026/9nhe_49410.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      44      5.49       5
     Mg      1      5.21       5
     S      39      5.16       5
     C    5443      2.51       5
     N    1501      2.21       5
     O    1750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8778
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 5941
          Classifications: {'peptide': 736}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 700}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 476
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "C"
      Number of atoms: 459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 459
          Classifications: {'RNA': 22}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "F"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1901
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 13, 'TRANS': 222}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.79, per 1000 atoms: 0.20
  Number of scatterers: 8778
  At special positions: 0
  Unit cell: (106.47, 89.18, 108.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      44     15.00
     Mg      1     11.99
     O    1750      8.00
     N    1501      7.00
     C    5443      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 286.2 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      40.4% alpha, 17.5% beta
      14 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 190
      removed outlier: 3.564A  pdb=" N   ARG A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
      removed outlier: 3.625A  pdb=" N   LEU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 317 through 329
    Processing helix  chain 'A' and resid 333 through 342
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.966A  pdb=" N   ARG A 409 " --> pdb=" O   PRO A 405 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A 410 " --> pdb=" O   ARG A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 431 through 434
      removed outlier: 4.052A  pdb=" N   ALA A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 431 through 434'
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.632A  pdb=" N   MET A 439 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 467
    Processing helix  chain 'A' and resid 467 through 477
      removed outlier: 3.502A  pdb=" N   VAL A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 522
      removed outlier: 3.568A  pdb=" N   THR A 516 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ARG A 517 " --> pdb=" O   GLY A 514 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ASP A 518 " --> pdb=" O   TRP A 515 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   MET A 519 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG A 520 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER A 521 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS A 522 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 513 through 522'
    Processing helix  chain 'A' and resid 541 through 560
    Processing helix  chain 'A' and resid 575 through 590
    Processing helix  chain 'A' and resid 604 through 616
      removed outlier: 3.606A  pdb=" N   CYS A 614 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 650
      removed outlier: 3.505A  pdb=" N   LEU A 650 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 729
    Processing helix  chain 'A' and resid 743 through 745
      No H-bonds generated for 'chain 'A' and resid 743 through 745'
    Processing helix  chain 'A' and resid 746 through 752
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 853
    Processing helix  chain 'A' and resid 867 through 880
      removed outlier: 3.809A  pdb=" N   GLN A 871 " --> pdb=" O   PRO A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 893
      removed outlier: 3.708A  pdb=" N   ASN A 893 " --> pdb=" O   TYR A 890 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 110
      removed outlier: 3.766A  pdb=" N   GLU F  93 " --> pdb=" O   MET F  89 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP F  94 " --> pdb=" O   LYS F  90 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP F  99 " --> pdb=" O   ASN F  95 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN F 101 " --> pdb=" O   LYS F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 112 through 115
    Processing helix  chain 'F' and resid 166 through 178
    Processing helix  chain 'F' and resid 190 through 199
    Processing helix  chain 'F' and resid 218 through 233
      removed outlier: 3.740A  pdb=" N   ASP F 223 " --> pdb=" O   PRO F 219 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ALA F 224 " --> pdb=" O   GLU F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 260
    Processing helix  chain 'F' and resid 271 through 279
      removed outlier: 4.064A  pdb=" N   THR F 275 " --> pdb=" O   SER F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 290 through 296
      removed outlier: 3.652A  pdb=" N   GLU F 294 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER F 295 " --> pdb=" O   GLU F 291 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 323
      removed outlier: 4.019A  pdb=" N   ARG F 317 " --> pdb=" O   THR F 313 " (cutoff:3.500A)
      Proline residue:  F 320  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 267
      removed outlier: 3.575A  pdb=" N   THR A 294 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 303 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 161 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LYS A 480 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208
      removed outlier: 3.663A  pdb=" N   ASP A 174 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 372
      removed outlier: 3.551A  pdb=" N   GLU A 375 " --> pdb=" O   MET A 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 402
    Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.570A  pdb=" N   ARG A 491 " --> pdb=" O   VAL A 802 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 801 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER A 831 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 735 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ARG A 739 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500
      removed outlier: 3.553A  pdb=" N   GLN A 500 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571
      removed outlier: 7.903A  pdb=" N   VAL A 569 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 535 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   THR A 537 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   CYS A 597 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 156
      removed outlier: 6.903A  pdb=" N   GLN F 142 " --> pdb=" O   LYS F 150 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL F 140 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   HIS F 154 " --> pdb=" O   PHE F 138 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   PHE F 138 " --> pdb=" O   HIS F 154 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   THR F 156 " --> pdb=" O   GLY F 136 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   GLY F 136 " --> pdb=" O   THR F 156 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL F 120 " --> pdb=" O   THR F 141 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   PHE F 216 " --> pdb=" O   ASP F 117 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR F 119 " --> pdb=" O   PHE F 216 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   MET F 215 " --> pdb=" O   TYR F 246 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 0.92 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1542
        1.32 -     1.45: 2477
        1.45 -     1.57: 4882
        1.57 -     1.70: 86
        1.70 -     1.82: 61
  Bond restraints: 9048
  Sorted by residual:
  bond pdb=" C5'   A C  20 "
       pdb=" C4'   A C  20 "
    ideal  model  delta    sigma   weight residual
    1.508  1.541 -0.033 7.00e-03 2.04e+04 2.28e+01
  bond pdb=" C5'   A C  12 "
       pdb=" C4'   A C  12 "
    ideal  model  delta    sigma   weight residual
    1.508  1.540 -0.032 7.00e-03 2.04e+04 2.14e+01
  bond pdb=" C5'   G B   5 "
       pdb=" C4'   G B   5 "
    ideal  model  delta    sigma   weight residual
    1.508  1.539 -0.031 7.00e-03 2.04e+04 1.91e+01
  bond pdb=" C4    C B  11 "
       pdb=" N4    C B  11 "
    ideal  model  delta    sigma   weight residual
    1.335  1.296  0.039 9.00e-03 1.23e+04 1.87e+01
  bond pdb=" C4    C C  17 "
       pdb=" N4    C C  17 "
    ideal  model  delta    sigma   weight residual
    1.335  1.297  0.038 9.00e-03 1.23e+04 1.77e+01
  ... (remaining 9043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 10841
        2.23 -     4.47: 1405
        4.47 -     6.70: 182
        6.70 -     8.93: 19
        8.93 -    11.16: 5
  Bond angle restraints: 12452
  Sorted by residual:
  angle pdb=" O5'   A C  20 "
        pdb=" C5'   A C  20 "
        pdb=" C4'   A C  20 "
      ideal   model   delta    sigma   weight residual
     109.40  117.87   -8.47 8.00e-01 1.56e+00 1.12e+02
  angle pdb=" O4'   C B  11 "
        pdb=" C1'   C B  11 "
        pdb=" N1    C B  11 "
      ideal   model   delta    sigma   weight residual
     108.50  115.55   -7.05 7.00e-01 2.04e+00 1.01e+02
  angle pdb=" C3'   C C  10 "
        pdb=" O3'   C C  10 "
        pdb=" P     C C  11 "
      ideal   model   delta    sigma   weight residual
     119.70  108.54   11.16 1.20e+00 6.94e-01 8.65e+01
  angle pdb=" N6    A B  12 "
        pdb=" C6    A B  12 "
        pdb=" N1    A B  12 "
      ideal   model   delta    sigma   weight residual
     118.60  113.09    5.51 6.00e-01 2.78e+00 8.42e+01
  angle pdb=" C3'   C C   8 "
        pdb=" O3'   C C   8 "
        pdb=" P     A C   9 "
      ideal   model   delta    sigma   weight residual
     119.70  109.07   10.63 1.20e+00 6.94e-01 7.84e+01
  ... (remaining 12447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.89: 5197
       27.89 -    55.77: 265
       55.77 -    83.66: 68
       83.66 -   111.54: 5
      111.54 -   139.43: 1
  Dihedral angle restraints: 5536
    sinusoidal: 2681
      harmonic: 2855
  Sorted by residual:
  dihedral pdb=" C5'   U B   1 "
           pdb=" C4'   U B   1 "
           pdb=" C3'   U B   1 "
           pdb=" O3'   U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   95.09   51.91     1      8.00e+00 1.56e-02 5.75e+01
  dihedral pdb=" O4'   C C   8 "
           pdb=" C2'   C C   8 "
           pdb=" C1'   C C   8 "
           pdb=" C3'   C C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -25.84   50.84     1      8.00e+00 1.56e-02 5.53e+01
  dihedral pdb=" O4'   U B   1 "
           pdb=" C4'   U B   1 "
           pdb=" C3'   U B   1 "
           pdb=" C2'   U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -19.90   43.90     1      8.00e+00 1.56e-02 4.19e+01
  ... (remaining 5533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1278
       0.121 -    0.243: 137
       0.243 -    0.364: 15
       0.364 -    0.485: 7
       0.485 -    0.607: 2
  Chirality restraints: 1439
  Sorted by residual:
  chirality pdb=" P     A C  25 "
            pdb=" OP1   A C  25 "
            pdb=" OP2   A C  25 "
            pdb=" O5'   A C  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.02   -0.61 2.00e-01 2.50e+01 9.20e+00
  chirality pdb=" P     U B   1 "
            pdb=" OP1   U B   1 "
            pdb=" OP2   U B   1 "
            pdb=" O5'   U B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" P     A C   5 "
            pdb=" OP1   A C   5 "
            pdb=" OP2   A C   5 "
            pdb=" O5'   A C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.81   -0.40 2.00e-01 2.50e+01 4.06e+00
  ... (remaining 1436 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  14 "   -0.198 2.00e-02 2.50e+03   9.51e-02 2.03e+02
        pdb=" N1    U C  14 "    0.067 2.00e-02 2.50e+03
        pdb=" C2    U C  14 "    0.087 2.00e-02 2.50e+03
        pdb=" O2    U C  14 "    0.021 2.00e-02 2.50e+03
        pdb=" N3    U C  14 "    0.033 2.00e-02 2.50e+03
        pdb=" C4    U C  14 "   -0.023 2.00e-02 2.50e+03
        pdb=" O4    U C  14 "   -0.129 2.00e-02 2.50e+03
        pdb=" C5    U C  14 "    0.048 2.00e-02 2.50e+03
        pdb=" C6    U C  14 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  13 "    0.184 2.00e-02 2.50e+03   8.40e-02 1.94e+02
        pdb=" N9    A B  13 "    0.010 2.00e-02 2.50e+03
        pdb=" C8    A B  13 "   -0.098 2.00e-02 2.50e+03
        pdb=" N7    A B  13 "   -0.072 2.00e-02 2.50e+03
        pdb=" C5    A B  13 "   -0.019 2.00e-02 2.50e+03
        pdb=" C6    A B  13 "    0.044 2.00e-02 2.50e+03
        pdb=" N6    A B  13 "    0.123 2.00e-02 2.50e+03
        pdb=" N1    A B  13 "    0.012 2.00e-02 2.50e+03
        pdb=" C2    A B  13 "   -0.058 2.00e-02 2.50e+03
        pdb=" N3    A B  13 "   -0.076 2.00e-02 2.50e+03
        pdb=" C4    A B  13 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  12 "    0.203 2.00e-02 2.50e+03   8.19e-02 1.84e+02
        pdb=" N9    A C  12 "   -0.065 2.00e-02 2.50e+03
        pdb=" C8    A C  12 "   -0.086 2.00e-02 2.50e+03
        pdb=" N7    A C  12 "   -0.020 2.00e-02 2.50e+03
        pdb=" C5    A C  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6    A C  12 "    0.038 2.00e-02 2.50e+03
        pdb=" N6    A C  12 "    0.085 2.00e-02 2.50e+03
        pdb=" N1    A C  12 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    A C  12 "   -0.040 2.00e-02 2.50e+03
        pdb=" N3    A C  12 "   -0.075 2.00e-02 2.50e+03
        pdb=" C4    A C  12 "   -0.060 2.00e-02 2.50e+03
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 26
        2.48 -     3.09: 6012
        3.09 -     3.69: 13819
        3.69 -     4.30: 18517
        4.30 -     4.90: 30441
  Nonbonded interactions: 68815
  Sorted by model distance:
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG C 101 "
     model   vdw
     1.880 2.170
  nonbonded pdb=" O3'   G C  15 "
            pdb="MG    MG C 101 "
     model   vdw
     2.034 2.170
  nonbonded pdb=" OD1 ASP A 451 "
            pdb=" OG  SER A 793 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" NE2 HIS A 192 "
            pdb=" O   TYR A 220 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   ASP A 393 "
            pdb=" NE2 GLN A 396 "
     model   vdw
     2.280 3.120
  ... (remaining 68810 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.048   9048  Z= 0.647
  Angle     :  1.496  11.163  12452  Z= 1.134
  Chirality :  0.083   0.607   1439
  Planarity :  0.013   0.125   1422
  Dihedral  : 17.066 139.426   3694
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.01 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.26), residues: 954
  helix: -0.44 (0.27), residues: 326
  sheet: -0.94 (0.38), residues: 169
  loop : -1.10 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 301 
 TYR   0.112   0.015   TYR A 607 
 PHE   0.061   0.008   PHE A 272 
 TRP   0.098   0.020   TRP A 655 
 HIS   0.010   0.002   HIS A 874 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00942 /  0.65 ( 9048)
  covalent geometry    : angle       1.49629 /  1.13 (12452)
  hydrogen bonds       : bond        0.20558 / 14.50 (  349)
  hydrogen bonds       : angle       7.54556 /  5.05 (  980)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 296
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASN cc_start: 0.7904 (t0) cc_final: 0.7639 (t0)
REVERT: A  300 ASP cc_start: 0.7867 (m-30) cc_final: 0.6631 (m-30)
REVERT: A  302 LEU cc_start: 0.8678 (tp) cc_final: 0.8468 (mt)
REVERT: A  303 LEU cc_start: 0.8192 (mp) cc_final: 0.7963 (mp)
REVERT: A  385 LYS cc_start: 0.8894 (tmtt) cc_final: 0.8448 (mmtp)
REVERT: A  389 LEU cc_start: 0.8601 (mt) cc_final: 0.8223 (mp)
REVERT: A  404 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7699 (mttm)
REVERT: A  412 LEU cc_start: 0.8865 (mm) cc_final: 0.8564 (mt)
REVERT: A  425 GLN cc_start: 0.7848 (tt0) cc_final: 0.7618 (mp10)
REVERT: A  608 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7914 (tm-30)
REVERT: A  625 VAL cc_start: 0.8494 (t) cc_final: 0.8172 (m)
REVERT: A  665 MET cc_start: 0.7292 (ttm) cc_final: 0.6687 (mtp)
REVERT: A  712 HIS cc_start: 0.4843 (t-90) cc_final: 0.4316 (t-170)
REVERT: A  734 ARG cc_start: 0.7312 (ttm110) cc_final: 0.6858 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8989 (tptp) cc_final: 0.8544 (mptt)
REVERT: A  842 ASN cc_start: 0.7229 (t0) cc_final: 0.6943 (t0)
REVERT: F   89 MET cc_start: 0.6891 (mmp) cc_final: 0.6501 (mmm)
REVERT: F  100 ILE cc_start: 0.8279 (mm) cc_final: 0.8016 (mm)
REVERT: F  105 LYS cc_start: 0.7697 (pptt) cc_final: 0.7462 (mttp)
REVERT: F  135 ILE cc_start: 0.7072 (pt) cc_final: 0.6569 (mm)
REVERT: F  177 PHE cc_start: 0.6792 (m-80) cc_final: 0.6088 (m-80)
REVERT: F  195 LEU cc_start: 0.8411 (mm) cc_final: 0.7939 (mt)
REVERT: F  201 TYR cc_start: 0.7345 (t80) cc_final: 0.6658 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 299
  average time/residue: 0.1250
  time to fit residues: 48.1092
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 GLN
F 197 ASN
F 231 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.164496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.142481 restraints weight = 16016.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.144503 restraints weight = 11632.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.146379 restraints weight = 8980.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.147509 restraints weight = 5868.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147805 restraints weight = 5309.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9048  Z= 0.179
  Angle     :  0.755   6.729  12452  Z= 0.410
  Chirality :  0.051   0.356   1439
  Planarity :  0.007   0.140   1422
  Dihedral  : 15.780 142.438   1741
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.04 %
    Favored  : 94.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.27), residues: 954
  helix: -0.03 (0.28), residues: 341
  sheet: -0.93 (0.39), residues: 185
  loop : -0.98 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 520 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.022   0.003   PHE F 177 
 TRP   0.013   0.002   TRP A 533 
 HIS   0.009   0.002   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 9048)
  covalent geometry    : angle       0.75511 /  0.41 (12452)
  hydrogen bonds       : bond        0.06373 /  4.25 (  349)
  hydrogen bonds       : angle       5.53322 /  3.72 (  980)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 214
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 GLU cc_start: 0.8505 (tt0) cc_final: 0.8296 (tp30)
REVERT: A  385 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8590 (mttm)
REVERT: A  404 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7887 (mptt)
REVERT: A  568 LEU cc_start: 0.7410 (pt) cc_final: 0.7151 (pt)
REVERT: A  578 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7088 (mp0)
REVERT: A  734 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6949 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8771 (tptp) cc_final: 0.8500 (mptt)
REVERT: A  780 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8651 (mtpp)
REVERT: F   89 MET cc_start: 0.6960 (mmp) cc_final: 0.6511 (mmm)
REVERT: F  105 LYS cc_start: 0.7700 (pptt) cc_final: 0.7465 (mttp)
REVERT: F  119 TYR cc_start: 0.5760 (m-80) cc_final: 0.5144 (m-10)
REVERT: F  177 PHE cc_start: 0.6682 (m-80) cc_final: 0.6169 (m-80)
REVERT: F  201 TYR cc_start: 0.7635 (t80) cc_final: 0.6967 (t80)
  outliers start: 6
  outliers final: 1
  residues processed: 217
  average time/residue: 0.1010
  time to fit residues: 29.8211
Evaluate side-chains
  158 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 5 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 459 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.163713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.141348 restraints weight = 15902.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.143128 restraints weight = 12044.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.145374 restraints weight = 8853.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.145999 restraints weight = 5869.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.146586 restraints weight = 5659.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9048  Z= 0.152
  Angle     :  0.659   8.061  12452  Z= 0.356
  Chirality :  0.047   0.252   1439
  Planarity :  0.005   0.054   1422
  Dihedral  : 15.536 142.188   1741
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.24 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.27), residues: 954
  helix:  0.11 (0.28), residues: 343
  sheet: -1.07 (0.37), residues: 193
  loop : -0.93 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 792 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.017   0.002   PHE A 561 
 TRP   0.012   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.15 ( 9048)
  covalent geometry    : angle       0.65929 /  0.36 (12452)
  hydrogen bonds       : bond        0.05423 /  3.64 (  349)
  hydrogen bonds       : angle       5.16516 /  3.42 (  980)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.7821 (tt) cc_final: 0.7502 (tt)
REVERT: A  292 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7013 (ttmt)
REVERT: A  381 GLU cc_start: 0.8559 (tt0) cc_final: 0.8288 (tp30)
REVERT: A  385 LYS cc_start: 0.8726 (tmtt) cc_final: 0.8417 (mttm)
REVERT: A  404 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8029 (mptt)
REVERT: A  542 ARG cc_start: 0.7745 (tpt90) cc_final: 0.7384 (tpt90)
REVERT: A  578 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7070 (mp0)
REVERT: A  734 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7098 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8785 (tptp) cc_final: 0.8498 (mptt)
REVERT: F  119 TYR cc_start: 0.5879 (m-80) cc_final: 0.5355 (m-10)
REVERT: F  177 PHE cc_start: 0.6828 (m-80) cc_final: 0.6409 (m-80)
REVERT: F  201 TYR cc_start: 0.7637 (t80) cc_final: 0.7079 (t80)
REVERT: F  254 THR cc_start: 0.8845 (p) cc_final: 0.8551 (p)
REVERT: F  285 THR cc_start: 0.7936 (p) cc_final: 0.7708 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1017
  time to fit residues: 29.5742
Evaluate side-chains
  155 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 746 GLN
F 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.160076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138083 restraints weight = 16388.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.140238 restraints weight = 12327.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.142055 restraints weight = 9549.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.142460 restraints weight = 6203.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.142597 restraints weight = 5967.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9048  Z= 0.174
  Angle     :  0.660   7.620  12452  Z= 0.354
  Chirality :  0.047   0.246   1439
  Planarity :  0.004   0.049   1422
  Dihedral  : 15.436 143.733   1741
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.55 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.27), residues: 954
  helix:  0.21 (0.28), residues: 343
  sheet: -1.18 (0.37), residues: 186
  loop : -0.91 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 406 
 TYR   0.030   0.002   TYR A 291 
 PHE   0.033   0.002   PHE F 253 
 TRP   0.019   0.003   TRP A 533 
 HIS   0.006   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 9048)
  covalent geometry    : angle       0.65974 /  0.35 (12452)
  hydrogen bonds       : bond        0.04990 /  3.39 (  349)
  hydrogen bonds       : angle       5.06572 /  3.36 (  980)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7536 (ttpt) cc_final: 0.7059 (ttmt)
REVERT: A  381 GLU cc_start: 0.8487 (tt0) cc_final: 0.8257 (tp30)
REVERT: A  385 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8417 (mmtp)
REVERT: A  404 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8051 (mttt)
REVERT: A  542 ARG cc_start: 0.7795 (tpt90) cc_final: 0.7418 (tpt90)
REVERT: A  578 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7041 (mp0)
REVERT: A  760 LYS cc_start: 0.8824 (tptp) cc_final: 0.8527 (mptt)
REVERT: F   89 MET cc_start: 0.7473 (mmm) cc_final: 0.7019 (mmm)
REVERT: F  119 TYR cc_start: 0.6049 (m-80) cc_final: 0.5286 (m-80)
REVERT: F  177 PHE cc_start: 0.6959 (m-80) cc_final: 0.6649 (m-80)
REVERT: F  201 TYR cc_start: 0.7661 (t80) cc_final: 0.6866 (t80)
REVERT: F  285 THR cc_start: 0.7966 (p) cc_final: 0.7736 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0958
  time to fit residues: 26.7482
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   chunk 72 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.162726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.140691 restraints weight = 16152.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.142329 restraints weight = 12442.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144388 restraints weight = 9358.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.145356 restraints weight = 6071.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.145488 restraints weight = 5527.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9048  Z= 0.127
  Angle     :  0.624   9.143  12452  Z= 0.330
  Chirality :  0.045   0.244   1439
  Planarity :  0.004   0.046   1422
  Dihedral  : 15.305 144.075   1741
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.75 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.27), residues: 954
  helix:  0.28 (0.28), residues: 345
  sheet: -1.01 (0.37), residues: 192
  loop : -0.77 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 792 
 TYR   0.041   0.002   TYR A 207 
 PHE   0.013   0.001   PHE F 267 
 TRP   0.010   0.002   TRP A 533 
 HIS   0.003   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 9048)
  covalent geometry    : angle       0.62361 /  0.33 (12452)
  hydrogen bonds       : bond        0.04625 /  3.18 (  349)
  hydrogen bonds       : angle       4.96125 /  3.28 (  980)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 210
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7413 (ttpt) cc_final: 0.7018 (ttmt)
REVERT: A  381 GLU cc_start: 0.8475 (tt0) cc_final: 0.8221 (tp30)
REVERT: A  385 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8345 (mmtp)
REVERT: A  404 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8054 (mttt)
REVERT: A  542 ARG cc_start: 0.7770 (tpt90) cc_final: 0.7534 (tpt90)
REVERT: A  568 LEU cc_start: 0.7806 (pt) cc_final: 0.7410 (pt)
REVERT: A  578 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6750 (mp0)
REVERT: A  760 LYS cc_start: 0.8722 (tptp) cc_final: 0.8507 (mptt)
REVERT: F   89 MET cc_start: 0.7556 (mmm) cc_final: 0.6992 (mmm)
REVERT: F  119 TYR cc_start: 0.5996 (m-80) cc_final: 0.5661 (m-10)
REVERT: F  177 PHE cc_start: 0.6984 (m-80) cc_final: 0.6558 (m-80)
REVERT: F  285 THR cc_start: 0.7787 (p) cc_final: 0.7521 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0933
  time to fit residues: 27.5909
Evaluate side-chains
  162 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 86 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 746 GLN
F 227 ASN
F 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.160289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.138260 restraints weight = 16339.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140555 restraints weight = 12179.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.142284 restraints weight = 9196.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.142851 restraints weight = 6083.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.142872 restraints weight = 5600.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9048  Z= 0.153
  Angle     :  0.638   7.561  12452  Z= 0.336
  Chirality :  0.046   0.238   1439
  Planarity :  0.004   0.050   1422
  Dihedral  : 15.205 144.512   1741
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.98 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.27), residues: 954
  helix:  0.35 (0.28), residues: 345
  sheet: -1.03 (0.36), residues: 190
  loop : -0.79 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 792 
 TYR   0.032   0.002   TYR A 291 
 PHE   0.012   0.001   PHE F 267 
 TRP   0.011   0.002   TRP A 533 
 HIS   0.003   0.001   HIS A 712 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 9048)
  covalent geometry    : angle       0.63829 /  0.34 (12452)
  hydrogen bonds       : bond        0.04635 /  3.21 (  349)
  hydrogen bonds       : angle       4.89936 /  3.27 (  980)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7479 (ttpt) cc_final: 0.7107 (ttmt)
REVERT: A  381 GLU cc_start: 0.8433 (tt0) cc_final: 0.8167 (tp30)
REVERT: A  385 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8299 (mmtp)
REVERT: A  404 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8100 (mttt)
REVERT: A  542 ARG cc_start: 0.7829 (tpt90) cc_final: 0.7555 (tpt90)
REVERT: A  578 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6862 (mp0)
REVERT: A  760 LYS cc_start: 0.8745 (tptp) cc_final: 0.8512 (mptt)
REVERT: F  177 PHE cc_start: 0.7097 (m-80) cc_final: 0.6678 (m-80)
REVERT: F  285 THR cc_start: 0.7735 (p) cc_final: 0.7510 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0877
  time to fit residues: 23.8750
Evaluate side-chains
  147 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0970
   chunk 73 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
F 227 ASN
F 257 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.161128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139321 restraints weight = 16329.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140897 restraints weight = 12245.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.143070 restraints weight = 9410.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.143921 restraints weight = 6362.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.144428 restraints weight = 5896.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9048  Z= 0.134
  Angle     :  0.624   6.971  12452  Z= 0.331
  Chirality :  0.045   0.236   1439
  Planarity :  0.004   0.044   1422
  Dihedral  : 15.137 144.643   1741
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.92 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.27), residues: 954
  helix:  0.33 (0.28), residues: 345
  sheet: -1.00 (0.37), residues: 188
  loop : -0.78 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 606 
 TYR   0.034   0.002   TYR A 291 
 PHE   0.011   0.001   PHE F 143 
 TRP   0.024   0.002   TRP A 477 
 HIS   0.002   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 9048)
  covalent geometry    : angle       0.62435 /  0.33 (12452)
  hydrogen bonds       : bond        0.04399 /  3.02 (  349)
  hydrogen bonds       : angle       4.87105 /  3.24 (  980)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7466 (ttpt) cc_final: 0.7098 (ttmt)
REVERT: A  381 GLU cc_start: 0.8371 (tt0) cc_final: 0.8040 (mm-30)
REVERT: A  385 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8263 (mmtp)
REVERT: A  404 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8051 (mttt)
REVERT: A  542 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7523 (tpt90)
REVERT: A  568 LEU cc_start: 0.7748 (pt) cc_final: 0.7368 (pt)
REVERT: A  578 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7111 (mp0)
REVERT: A  760 LYS cc_start: 0.8773 (tptp) cc_final: 0.8532 (mptt)
REVERT: F   89 MET cc_start: 0.6964 (mmt) cc_final: 0.6518 (mmm)
REVERT: F  177 PHE cc_start: 0.7076 (m-80) cc_final: 0.6627 (m-80)
REVERT: F  285 THR cc_start: 0.7673 (p) cc_final: 0.7432 (p)
REVERT: F  290 CYS cc_start: 0.7562 (p) cc_final: 0.7283 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0821
  time to fit residues: 23.8170
Evaluate side-chains
  155 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0870
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0060
   chunk 85 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5176

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 746 GLN
F 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.161828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140038 restraints weight = 16069.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.142036 restraints weight = 11868.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.144171 restraints weight = 8853.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.144472 restraints weight = 5970.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.144897 restraints weight = 5850.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.4902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9048  Z= 0.120
  Angle     :  0.609   8.106  12452  Z= 0.321
  Chirality :  0.044   0.234   1439
  Planarity :  0.004   0.043   1422
  Dihedral  : 15.112 144.671   1741
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.60 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.27), residues: 954
  helix:  0.39 (0.28), residues: 345
  sheet: -0.93 (0.37), residues: 186
  loop : -0.74 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 792 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.014   0.001   PHE F 143 
 TRP   0.012   0.002   TRP A 477 
 HIS   0.004   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 9048)
  covalent geometry    : angle       0.60912 /  0.32 (12452)
  hydrogen bonds       : bond        0.04110 /  2.84 (  349)
  hydrogen bonds       : angle       4.75491 /  3.16 (  980)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7428 (ttpt) cc_final: 0.7060 (ttmt)
REVERT: A  381 GLU cc_start: 0.8399 (tt0) cc_final: 0.8048 (mm-30)
REVERT: A  385 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8039 (mmtp)
REVERT: A  404 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8036 (mttt)
REVERT: A  515 TRP cc_start: 0.8261 (p90) cc_final: 0.7647 (p90)
REVERT: A  542 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7542 (tpt90)
REVERT: A  568 LEU cc_start: 0.7730 (pt) cc_final: 0.7363 (pt)
REVERT: A  578 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7097 (mp0)
REVERT: A  760 LYS cc_start: 0.8753 (tptp) cc_final: 0.8503 (mptt)
REVERT: A  861 SER cc_start: 0.8747 (p) cc_final: 0.8437 (p)
REVERT: F   89 MET cc_start: 0.6940 (mmt) cc_final: 0.6407 (mmm)
REVERT: F  177 PHE cc_start: 0.7067 (m-80) cc_final: 0.6607 (m-80)
REVERT: F  285 THR cc_start: 0.7633 (p) cc_final: 0.7418 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0879
  time to fit residues: 25.1753
Evaluate side-chains
  159 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 9 optimal weight:    9.9990
   chunk 24 optimal weight:    0.2980
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.158787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.136868 restraints weight = 16173.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138941 restraints weight = 12223.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.140720 restraints weight = 8983.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.141867 restraints weight = 5987.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142202 restraints weight = 5357.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9048  Z= 0.155
  Angle     :  0.647   6.707  12452  Z= 0.340
  Chirality :  0.045   0.231   1439
  Planarity :  0.004   0.044   1422
  Dihedral  : 15.082 144.829   1741
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.15 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.27), residues: 954
  helix:  0.32 (0.28), residues: 346
  sheet: -1.09 (0.36), residues: 192
  loop : -0.76 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 606 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.065   0.002   PHE F 312 
 TRP   0.011   0.002   TRP A 166 
 HIS   0.003   0.001   HIS A 874 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 9048)
  covalent geometry    : angle       0.64705 /  0.34 (12452)
  hydrogen bonds       : bond        0.04474 /  3.09 (  349)
  hydrogen bonds       : angle       4.82661 /  3.22 (  980)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7442 (ttpt) cc_final: 0.7060 (ttmt)
REVERT: A  324 GLU cc_start: 0.7841 (pp20) cc_final: 0.7435 (tm-30)
REVERT: A  381 GLU cc_start: 0.8393 (tt0) cc_final: 0.8037 (mm-30)
REVERT: A  385 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8069 (mttm)
REVERT: A  404 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8056 (mttt)
REVERT: A  515 TRP cc_start: 0.8381 (p90) cc_final: 0.7791 (p90)
REVERT: A  542 ARG cc_start: 0.7811 (tpt90) cc_final: 0.7530 (tpt90)
REVERT: A  568 LEU cc_start: 0.7753 (pt) cc_final: 0.7374 (pt)
REVERT: A  578 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7068 (mp0)
REVERT: A  760 LYS cc_start: 0.8724 (tptp) cc_final: 0.8468 (mptt)
REVERT: A  861 SER cc_start: 0.8934 (p) cc_final: 0.8576 (p)
REVERT: F   89 MET cc_start: 0.6979 (mmt) cc_final: 0.6644 (tpp)
REVERT: F  177 PHE cc_start: 0.7056 (m-80) cc_final: 0.6569 (m-80)
REVERT: F  285 THR cc_start: 0.7687 (p) cc_final: 0.7432 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0930
  time to fit residues: 26.2537
Evaluate side-chains
  157 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0060
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.161134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.139545 restraints weight = 16107.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.141948 restraints weight = 12336.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.143567 restraints weight = 9310.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.144453 restraints weight = 6072.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.144854 restraints weight = 5462.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.5317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9048  Z= 0.126
  Angle     :  0.637   8.532  12452  Z= 0.335
  Chirality :  0.045   0.232   1439
  Planarity :  0.005   0.064   1422
  Dihedral  : 15.123 144.986   1741
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.46 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.27), residues: 954
  helix:  0.31 (0.28), residues: 345
  sheet: -1.07 (0.36), residues: 194
  loop : -0.62 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 823 
 TYR   0.026   0.002   TYR A 291 
 PHE   0.058   0.002   PHE F 312 
 TRP   0.010   0.001   TRP A 533 
 HIS   0.002   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 9048)
  covalent geometry    : angle       0.63739 /  0.33 (12452)
  hydrogen bonds       : bond        0.04162 /  2.88 (  349)
  hydrogen bonds       : angle       4.74611 /  3.16 (  980)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7861 (pp20) cc_final: 0.7462 (tm-30)
REVERT: A  381 GLU cc_start: 0.8271 (tt0) cc_final: 0.7947 (mm-30)
REVERT: A  385 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8128 (mmtp)
REVERT: A  404 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8037 (mttt)
REVERT: A  515 TRP cc_start: 0.8368 (p90) cc_final: 0.7709 (p90)
REVERT: A  542 ARG cc_start: 0.7705 (tpt90) cc_final: 0.7289 (tpt90)
REVERT: A  568 LEU cc_start: 0.7793 (pt) cc_final: 0.7450 (pt)
REVERT: A  578 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7070 (mp0)
REVERT: A  760 LYS cc_start: 0.8737 (tptp) cc_final: 0.8504 (mptt)
REVERT: A  861 SER cc_start: 0.8779 (p) cc_final: 0.8490 (p)
REVERT: F   89 MET cc_start: 0.7020 (mmt) cc_final: 0.6669 (tpp)
REVERT: F  177 PHE cc_start: 0.7018 (m-80) cc_final: 0.6507 (m-80)
REVERT: F  285 THR cc_start: 0.7558 (p) cc_final: 0.7329 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0866
  time to fit residues: 24.4747
Evaluate side-chains
  160 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0770
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.3938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.162563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.141039 restraints weight = 15923.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.144100 restraints weight = 11950.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.145850 restraints weight = 8409.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.146072 restraints weight = 5569.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.146122 restraints weight = 5267.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.5432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9048  Z= 0.118
  Angle     :  0.613  10.261  12452  Z= 0.321
  Chirality :  0.044   0.231   1439
  Planarity :  0.004   0.043   1422
  Dihedral  : 15.081 145.441   1741
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.46 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.28), residues: 954
  helix:  0.37 (0.28), residues: 344
  sheet: -0.91 (0.37), residues: 194
  loop : -0.61 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 309 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.058   0.001   PHE F 312 
 TRP   0.010   0.001   TRP A 533 
 HIS   0.002   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 9048)
  covalent geometry    : angle       0.61284 /  0.32 (12452)
  hydrogen bonds       : bond        0.03984 /  2.76 (  349)
  hydrogen bonds       : angle       4.66979 /  3.12 (  980)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1463.86 seconds
wall clock time: 26 minutes 13.94 seconds (1573.94 seconds total)